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I am trying to understand the working of MutSigCV. But I am not sure about some terms used in MAF file format which is category.

According to MutSigCV, every mutation can be divided into the following categories:

  1. CpG transitions
  2. CpG transversions
  3. C: G transitions
  4. C: G transversions
  5. A: T transitions
  6. A: T transversions
  7. null+indel mutations

I am very much clear about some of this categories like C: G transitions and A: T transitions but for rest, I am unable to make any solid conceptual background. Can anyone suggest me the proper definition of these categories of mutations with proper examples?

Thanks.


Definition

MutSig stands for "Mutation Significance" and is defined here

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  • $\begingroup$ Did you try asking on the help forum? Or your problem is what is each mutation? $\endgroup$
    – llrs
    Jul 9, 2018 at 11:39
  • $\begingroup$ @Llopis: Not yet. I even didn't know about that. I know only GATK forum and this website. I have googled these terms extensively but didn't get even proper definitions. That's why I started the bounty on this question. $\endgroup$ Jul 9, 2018 at 12:35
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    $\begingroup$ CpG transversions are the same as C: G transversions, except that they are followed by a G which means they are potential targets for DNA methylation. Methylcytosine can undergo deamination to Thymine, which makes them mutation hotspots $\endgroup$ Jul 10, 2018 at 14:43
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    $\begingroup$ indel = insertion/deletion. I have no idea what null means in this context $\endgroup$ Jul 10, 2018 at 14:49
  • $\begingroup$ @heathobrien Those comments are an answer! With a link to a source you could get the bounty $\endgroup$
    – llrs
    Jul 11, 2018 at 9:03

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